I came from a Gen I FJR to the Gen I Super Ten, now have a Gen II Super Ten. I do not buy a new bike lightly. I put 162k miles on the '04 FJR Abs bike, taking it everywhere from river crossings to single track to uber speeds in Death Valley and close courses. I got the Super Ten with an upcoming Alaska trip in mind. For a while, I owned both. And yes, once you get used to the more relaxed ergos of the Super Ten, the FJR seems way too cramped. It felt like I had to pull my legs up sooooo high to get my feet on the pegs, compared to the Super Ten and the cockpit was just a lot more cramped.
I loved my FJR. I missed the perfectly dialed in custom suspension and the ability to warp time and space during a high speed pass. But we all get older too, and the more Sport-Touring riding position was not as comfortable as the Super Ten's sit up a beg position. There isn't anything the FJR did that the Super Ten can't do well, with the exception of supra legal speeds and brute power. Toss some street rubber on a Super Ten and it will keep up with the FJR just fine in the real world. Hey, it's the rider, not the bike. ;D
So the real question comes down to what kind of riding are you doing with the Super Ten? And how comfortable are the ergos of the FJR for you? If you mostly ride street now, that part is simple. If the ergos of the FJR are comfy for you, or will be with some risers, fine.
Now, do you want to live with side loading saddlebags? The Feej has big bags, and liners come with, but still, I don't miss the side opening bags. Now if you ride sans luggage most of the time, just enjoying day rides and not needing the cargo space, this may be moot.
The Feej has better weather protection, imho. But not night and day better, just a bit better. And yeah, I do miss that power adjustable windscreen sometimes. All the way down all summer, then up to that sweet spot in the fall where the rain just sheets off my helmet visor and up all the way for a real frog strangler.
Everything else is just farkles.